I haven't messed with my windshield yet, but you might try a popsicle stick or something like that. Or one of the special tools for working on windshield rubber installation, like a bent metal rod with a ball end.
Similar to this Your second picture looks like the edge of the weatherstrip is curled under and maybe hanging up on the metal. Work a tool under there and see if you can pull it outward. Maybe some mild heat would help.
I'm sure that one of the guys who've been where you are will be along to suggest more.
